Zinc in PDB 6tmb: Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases

The structure of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmb was solved by H.-K.S.Leiros, T.Christopeit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.60 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.590, 79.026, 67.235, 90.00, 130.09, 90.00
R / Rfree (%)	13.9 / 16.8

The structure of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases (pdb code 6tmb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.8 occ:1.00 HO A:OH404 1.8 16.4 1.0 ND1 A:HIS118 2.0 11.6 1.0 O A:OH404 2.0 13.7 1.0 NE2 A:HIS196 2.0 11.6 1.0 NE2 A:HIS116 2.1 11.3 1.0 HB2 A:HIS118 2.9 13.8 1.0 CE1 A:HIS118 3.0 13.2 1.0 CE1 A:HIS196 3.0 13.1 1.0 CD2 A:HIS196 3.0 9.9 1.0 CG A:HIS118 3.0 12.3 1.0 CE1 A:HIS116 3.0 11.4 1.0 CD2 A:HIS116 3.1 11.1 1.0 HE1 A:HIS118 3.1 15.9 1.0 HD2 A:HIS196 3.2 11.9 1.0 HE1 A:HIS196 3.2 15.7 1.0 HE1 A:HIS116 3.2 13.7 1.0 HD2 A:HIS116 3.2 13.3 1.0 CB A:HIS118 3.3 11.5 1.0 O A:HOH597 3.5 40.0 1.0 ZN A:ZN402 3.5 14.9 1.0 HB3 A:HIS118 3.6 13.8 1.0 HB2 A:CYS221 3.7 14.2 1.0 HB3 A:CYS221 3.9 14.2 1.0 O A:HOH701 3.9 16.0 1.0 OD1 A:ASP120 3.9 16.2 1.0 ND1 A:HIS196 4.1 11.5 1.0 NE2 A:HIS118 4.1 14.6 1.0 CB A:CYS221 4.1 11.9 1.0 CD2 A:HIS118 4.1 13.3 1.0 CG A:HIS196 4.1 9.8 1.0 ND1 A:HIS116 4.1 11.7 1.0 O A:HOH558 4.1 40.1 1.0 CG A:HIS116 4.2 11.1 1.0 SG A:CYS221 4.2 12.6 1.0 OD2 A:ASP120 4.5 15.3 1.0 H A:HIS118 4.5 12.7 1.0 CG A:ASP120 4.6 15.4 1.0 HG2 A:ARG121 4.7 12.7 1.0 HB3 A:SER197 4.7 14.8 1.0 CA A:HIS118 4.8 11.7 1.0 HE A:ARG121 4.8 14.9 1.0 HD1 A:HIS196 4.8 13.8 1.0 HE2 A:HIS118 4.8 17.5 1.0 HG3 A:ARG121 4.9 12.7 1.0 HD1 A:HIS116 4.9 14.0 1.0 HD2 A:HIS118 4.9 16.0 1.0

Zinc binding site 2 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.9 occ:1.00 HO A:OH404 2.0 16.4 1.0 O A:OH404 2.1 13.7 1.0 NE2 A:HIS263 2.1 11.7 1.0 OD2 A:ASP120 2.2 15.3 1.0 SG A:CYS221 2.2 12.6 1.0 O A:HOH701 2.2 16.0 1.0 CD2 A:HIS263 3.0 12.2 1.0 CE1 A:HIS263 3.1 12.6 1.0 HB3 A:CYS221 3.2 14.2 1.0 HH21 A:ARG121 3.2 17.4 1.0 HD2 A:HIS263 3.2 14.6 1.0 CG A:ASP120 3.2 15.4 1.0 HE1 A:HIS263 3.3 15.1 1.0 CB A:CYS221 3.3 11.9 1.0 ZN A:ZN401 3.5 13.8 1.0 HE A:ARG121 3.5 14.9 1.0 OD1 A:ASP120 3.6 16.2 1.0 HE1 A:HIS116 3.7 13.7 1.0 HB2 A:CYS221 3.8 14.2 1.0 O A:HOH558 3.8 40.1 1.0 NH2 A:ARG121 3.9 14.5 1.0 O A:HOH597 4.0 40.0 1.0 NE A:ARG121 4.2 12.4 1.0 CG A:HIS263 4.2 12.0 1.0 ND1 A:HIS263 4.2 12.1 1.0 HE1 A:HIS196 4.3 15.7 1.0 NE2 A:HIS196 4.3 11.6 1.0 O A:HOH621 4.4 16.1 1.0 CE1 A:HIS116 4.4 11.4 1.0 CE1 A:HIS196 4.4 13.1 1.0 O A:HOH793 4.4 44.4 1.0 HA A:CYS221 4.4 13.7 1.0 NE2 A:HIS116 4.4 11.3 1.0 CZ A:ARG121 4.5 13.6 1.0 HH22 A:ARG121 4.5 17.4 1.0 HA3 A:GLY262 4.5 14.7 1.0 CB A:ASP120 4.5 14.1 1.0 CA A:CYS221 4.5 11.4 1.0 HB2 A:ASP120 4.6 16.9 1.0 HB3 A:ASP120 4.8 16.9 1.0 HG2 A:ARG121 4.9 12.7 1.0 HD1 A:HIS263 5.0 14.5 1.0

Zinc binding site 3 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:17.9 occ:1.00 NE2 A:HIS170 2.0 19.1 1.0 CL A:CL405 2.2 40.5 1.0 CL A:CL406 2.3 43.6 1.0 CE1 A:HIS170 2.7 20.4 1.0 HE1 A:HIS170 2.7 24.4 1.0 CD2 A:HIS170 3.3 18.1 1.0 HB1 A:ALA135 3.5 16.9 1.0 HD2 A:HIS170 3.6 21.7 1.0 HB2 A:ALA135 3.7 16.9 1.0 ND1 A:HIS170 4.0 20.7 1.0 CB A:ALA135 4.1 14.1 1.0 CG A:HIS170 4.2 17.5 1.0 O A:HOH569 4.3 38.4 1.0 HA A:ALA135 4.4 16.2 1.0 HD1 A:HIS170 4.7 24.9 1.0 HG21 A:THR169 4.7 20.8 1.0 HB3 A:ALA135 4.8 16.9 1.0 CA A:ALA135 4.9 13.5 1.0 O A:HOH753 4.9 22.5 1.0 HG22 A:THR169 4.9 20.8 1.0

Zinc binding site 4 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.3 occ:1.00 O B:OH405 1.9 13.9 1.0 HO B:OH405 1.9 16.6 1.0 ND1 B:HIS118 2.0 13.4 1.0 NE2 B:HIS196 2.0 11.2 1.0 NE2 B:HIS116 2.1 12.0 1.0 HB2 B:HIS118 2.9 15.9 1.0 CE1 B:HIS118 2.9 15.9 1.0 CE1 B:HIS116 2.9 12.7 1.0 CG B:HIS118 3.0 13.6 1.0 CD2 B:HIS196 3.0 11.5 1.0 CE1 B:HIS196 3.0 12.5 1.0 HE1 B:HIS116 3.1 15.3 1.0 CD2 B:HIS116 3.1 11.2 1.0 HE1 B:HIS118 3.1 19.1 1.0 HD2 B:HIS196 3.1 13.8 1.0 HE1 B:HIS196 3.2 15.0 1.0 H4 B:9OB401 3.2 58.0 0.8 CB B:HIS118 3.3 13.2 1.0 HD2 B:HIS116 3.3 13.5 1.0 HB3 B:HIS118 3.5 15.9 1.0 H172 B:9OB401 3.6 57.8 0.8 ZN B:ZN403 3.6 15.5 1.0 N03 B:9OB401 3.7 48.3 0.8 HB2 B:CYS221 3.7 13.6 1.0 N18 B:9OB401 3.9 48.4 0.8 OD1 B:ASP120 4.0 15.2 1.0 HB3 B:CYS221 4.0 13.6 1.0 C17 B:9OB401 4.0 48.2 0.8 C02 B:9OB401 4.0 48.1 0.8 NE2 B:HIS118 4.0 15.8 1.0 CD2 B:HIS118 4.1 14.0 1.0 ND1 B:HIS116 4.1 11.9 1.0 ND1 B:HIS196 4.1 13.3 1.0 CG B:HIS196 4.1 12.8 1.0 CB B:CYS221 4.1 11.3 1.0 CG B:HIS116 4.2 10.6 1.0 SG B:CYS221 4.2 12.5 1.0 H B:HIS118 4.5 13.2 1.0 OD2 B:ASP120 4.6 14.3 1.0 N04 B:9OB401 4.6 48.3 0.8 O B:HOH550 4.7 27.0 1.0 HB3 B:SER197 4.7 13.4 1.0 CG B:ASP120 4.7 14.9 1.0 CA B:HIS118 4.7 12.0 1.0 HG2 B:ARG121 4.8 13.8 1.0 HE B:ARG121 4.8 17.1 1.0 HE2 B:HIS118 4.8 18.9 1.0 HD1 B:HIS116 4.8 14.3 1.0 HG3 B:ARG121 4.9 13.8 1.0 HD1 B:HIS196 4.9 15.9 1.0 H192 B:9OB401 4.9 57.9 0.8 HD2 B:HIS118 4.9 16.8 1.0 H171 B:9OB401 4.9 57.8 0.8

Zinc binding site 5 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:15.5 occ:1.00 HO B:OH405 2.0 16.6 1.0 N03 B:9OB401 2.1 48.3 0.8 NE2 B:HIS263 2.1 14.2 1.0 OD2 B:ASP120 2.1 14.3 1.0 SG B:CYS221 2.2 12.5 1.0 O B:OH405 2.3 13.9 1.0 N04 B:9OB401 2.7 48.3 0.8 H192 B:9OB401 2.8 57.9 0.8 HH21 B:ARG121 3.0 21.8 1.0 CD2 B:HIS263 3.1 12.7 1.0 CE1 B:HIS263 3.1 14.4 1.0 H4 B:9OB401 3.1 58.0 0.8 HB3 B:CYS221 3.2 13.6 1.0 HD2 B:HIS263 3.2 15.3 1.0 CG B:ASP120 3.2 14.9 1.0 C02 B:9OB401 3.2 48.1 0.8 HE1 B:HIS263 3.3 17.3 1.0 CB B:CYS221 3.4 11.3 1.0 HE B:ARG121 3.4 17.1 1.0 C19 B:9OB401 3.5 48.3 0.8 OD1 B:ASP120 3.6 15.2 1.0 ZN B:ZN402 3.6 14.3 1.0 N18 B:9OB401 3.6 48.4 0.8 HE1 B:HIS116 3.7 15.3 1.0 O B:HOH725 3.8 15.4 0.0 HB2 B:CYS221 3.8 13.6 1.0 H191 B:9OB401 3.8 57.9 0.8 NH2 B:ARG121 3.8 18.2 1.0 C17 B:9OB401 4.0 48.2 0.8 N05 B:9OB401 4.0 48.0 0.8 NE B:ARG121 4.2 14.2 1.0 ND1 B:HIS263 4.2 13.1 1.0 CG B:HIS263 4.2 12.4 1.0 NE2 B:HIS196 4.2 11.2 1.0 C01 B:9OB401 4.3 47.9 0.8 HE1 B:HIS196 4.3 15.0 1.0 CE1 B:HIS116 4.4 12.7 1.0 O B:HOH548 4.4 14.4 1.0 HH22 B:ARG121 4.4 21.8 1.0 H172 B:9OB401 4.4 57.8 0.8 CE1 B:HIS196 4.5 12.5 1.0 CZ B:ARG121 4.5 17.1 1.0 HA B:CYS221 4.5 13.3 1.0 H211 B:9OB401 4.5 57.3 0.8 CB B:ASP120 4.5 15.1 1.0 NE2 B:HIS116 4.6 12.0 1.0 CA B:CYS221 4.6 11.1 1.0 HA3 B:GLY262 4.6 14.5 1.0 HB2 B:ASP120 4.6 18.1 1.0 H171 B:9OB401 4.8 57.8 0.8 HB3 B:ASP120 4.8 18.1 1.0 C20 B:9OB401 4.8 48.0 0.8 HG2 B:ARG121 4.9 13.8 1.0 HD1 B:HIS263 5.0 15.7 1.0

Zinc binding site 6 out of 6 in the Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vim-2_1DI-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:15.2 occ:1.00 NE2 B:HIS170 2.0 13.6 1.0 CL B:CL407 2.2 41.8 1.0 CL B:CL406 2.2 19.7 1.0 CE1 B:HIS170 2.9 15.5 1.0 HE1 B:HIS170 3.0 18.6 1.0 CD2 B:HIS170 3.1 12.7 1.0 O B:HOH580 3.2 62.4 1.0 HD2 B:HIS170 3.3 15.3 1.0 HB1 B:ALA135 3.6 15.0 1.0 HB2 B:ALA135 3.9 15.0 1.0 ND1 B:HIS170 4.0 14.9 1.0 HG21 B:THR169 4.1 18.3 1.0 CG B:HIS170 4.2 13.3 1.0 CB B:ALA135 4.2 12.5 1.0 O B:HOH762 4.2 50.3 1.0 HA B:ALA135 4.5 13.8 1.0 HG22 B:THR169 4.6 18.3 1.0 HD1 B:HIS170 4.8 17.9 1.0 CG2 B:THR169 4.8 15.3 1.0 HB3 B:ALA135 4.9 15.0 1.0 CA B:ALA135 5.0 11.5 1.0

H.-K.S.Leiros, H.-K.S.Leiros, T.Christopeit. N/A N/A.